Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

High mobility group protein B1

Gene

HMGB1

Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Multifunctional redox sensitive protein with various roles in different cellular compartments. Nuclear functions are attributed to fully reduced HGMB1. Associates with chromatin and binds DNA with a preference to non-canonical DNA structures such as single-stranded DNA, DNA-containing cruciforms or bent structures, supercoiled DNA and ZDNA. Can bent DNA and enhance DNA flexibility by looping thus providing a mechanism to promote activities on various gene promoters. Can restructure the canonical nucleosome. Proposed to be an universal biosensor for nucleic acids. May promote inflammatory response to sterile and infectious signals and may be involved in the coordination and integration of innate and adaptive immune responses. In the cytoplasm may function as sensor and/or chaperone for immunogenic nucleic acids, and mediate autophagy. May act as danger associated molecular pattern (DAMP) molecule that amplifies immune responses during tissue injury.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei3 – 31Involved in intramolecular interaction with the C-terminal acidic tail

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi9 – 7971HMG box 1PROSITE-ProRule annotationAdd
BLAST
DNA bindingi95 – 16369HMG box 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Immunity, Inflammatory response, Innate immunity

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-GGA-211227. Activation of DNA fragmentation factor.

Names & Taxonomyi

Protein namesi
Recommended name:
High mobility group protein B1
Alternative name(s):
High mobility group protein 1
Short name:
HMG-1
Gene namesi
Name:HMGB1
Synonyms:HMG1
ORF Names:RCJMB04_15a21
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
Proteomesi
  • UP000000539 Componenti: Chromosome 1

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation1 Publication
  • Chromosome 1 Publication
  • Cytoplasm Curated
  • Secreted Curated

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Nucleus, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi3 – 31K → A: Impairs binding to distorted DNA; when associated with A-12. 1 Publication
Mutagenesisi12 – 121K → A: Impairs binding to distorted DNA; when associated with A-3. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 215214High mobility group protein B1PRO_0000423460Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi23 ↔ 45In disulfide HMGB1By similarity
Modified residuei23 – 231Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB1; alternateBy similarity
Modified residuei45 – 451Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB1; alternateBy similarity
Modified residuei106 – 1061Cysteine derivative; cysteine sulfonic acid (-SO(3)H) in sulfonyl HMGB1; alternateBy similarity

Post-translational modificationi

Reduction/oxidation of cysteine residues Cys-23, Cys-45 and Cys-106 and a possible intramolecular disulfide bond involving Cys-23 and Cys-45 give rise to different redox forms with specific functional activities: 1- fully reduced HMGB1 (HMGB1C23hC45hC106h), 2- disulfide HMGB1 (HMGB1C23-C45C106h) and 3- sulfonyl HMGB1 (HMGB1C23soC45soC106so).By similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ9YH06.

Expressioni

Gene expression databases

BgeeiENSGALG00000017082.

Interactioni

Protein-protein interaction databases

STRINGi9031.ENSGALP00000027541.

Structurei

3D structure databases

ProteinModelPortaliQ9YH06.
SMRiQ9YH06. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni27 – 4317NLS 1By similarityAdd
BLAST
Regioni178 – 1847NLS 2By similarity
Regioni196 – 21015Involved in intramolecular interaction with K-3Add
BLAST
Regioni211 – 2155Involved in interaction with histone H3

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi27 – 4317Nuclear localization signal (NLS) 1By similarityAdd
BLAST
Motifi178 – 1847Nuclear localization signal (NLS) 2By similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi186 – 21530Asp/Glu-rich (acidic)Add
BLAST

Domaini

The acidic C-terminal domain forms a flexible structure which can reversibly interact intramolecularily with the HMG boxes and modulate binding to DNA and other proteins; may involve Lys-3 and histone H3 'Lys-37' and 'Lys-38'.By similarity1 Publication

Sequence similaritiesi

Belongs to the HMGB family.Curated
Contains 2 HMG box DNA-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiQ9YH06.
KOiK10802.
OMAiAFFFYSQ.
OrthoDBiEOG091G0P81.
PhylomeDBiQ9YH06.
TreeFamiTF105371.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031076. HMGB1.
[Graphical view]
PANTHERiPTHR13711:SF157. PTHR13711:SF157. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9YH06-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK
60 70 80 90 100
TMSSKEKGKF EDMAKADKLR YEKEMKNYVP PKGETKKKFK DPNAPKRPPS
110 120 130 140 150
AFFLFCSEFR PKIKGEHPGL SIGDVAKKLG EMWNNTAADD KQPYEKKAAK
160 170 180 190 200
LKEKYEKDIA AYRAKGKVDA GKKVVAKAEK SKKKKEEEED EDEDEEDEED
210
EEEEEEEEED DDDDE
Length:215
Mass (Da):24,909
Last modified:May 1, 1999 - v1
Checksum:i3731F50262DCB1C3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti214 – 2141Missing in AAD52670 (PubMed:10978508).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y17968 mRNA. Translation: CAA76978.1.
AJ851648 mRNA. Translation: CAH65282.1.
AF178849 Genomic DNA. Translation: AAD52670.1.
AADN03000868 Genomic DNA. No translation available.
AADN03001640 Genomic DNA. No translation available.
JQ040530 mRNA. Translation: AFD33645.1.
RefSeqiNP_990233.1. NM_204902.2.
XP_015133153.1. XM_015277667.1.
XP_015133156.1. XM_015277670.1.
UniGeneiGga.4638.

Genome annotation databases

EnsembliENSGALT00000027593; ENSGALP00000027541; ENSGALG00000017082.
GeneIDi395724.
KEGGigga:395724.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y17968 mRNA. Translation: CAA76978.1.
AJ851648 mRNA. Translation: CAH65282.1.
AF178849 Genomic DNA. Translation: AAD52670.1.
AADN03000868 Genomic DNA. No translation available.
AADN03001640 Genomic DNA. No translation available.
JQ040530 mRNA. Translation: AFD33645.1.
RefSeqiNP_990233.1. NM_204902.2.
XP_015133153.1. XM_015277667.1.
XP_015133156.1. XM_015277670.1.
UniGeneiGga.4638.

3D structure databases

ProteinModelPortaliQ9YH06.
SMRiQ9YH06. Positions 5-166.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9031.ENSGALP00000027541.

Proteomic databases

PaxDbiQ9YH06.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000027593; ENSGALP00000027541; ENSGALG00000017082.
GeneIDi395724.
KEGGigga:395724.

Organism-specific databases

CTDi3146.

Phylogenomic databases

eggNOGiKOG0381. Eukaryota.
COG5648. LUCA.
GeneTreeiENSGT00760000119164.
HOGENOMiHOG000197861.
HOVERGENiHBG009000.
InParanoidiQ9YH06.
KOiK10802.
OMAiAFFFYSQ.
OrthoDBiEOG091G0P81.
PhylomeDBiQ9YH06.
TreeFamiTF105371.

Enzyme and pathway databases

ReactomeiR-GGA-211227. Activation of DNA fragmentation factor.

Miscellaneous databases

PROiQ9YH06.

Gene expression databases

BgeeiENSGALG00000017082.

Family and domain databases

Gene3Di1.10.30.10. 2 hits.
InterProiIPR009071. HMG_box_dom.
IPR017967. HMG_boxA_CS.
IPR031076. HMGB1.
[Graphical view]
PANTHERiPTHR13711:SF157. PTHR13711:SF157. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF09011. HMG_box_2. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 2 hits.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 2 hits.
PROSITEiPS00353. HMG_BOX_1. 1 hit.
PS50118. HMG_BOX_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiHMGB1_CHICK
AccessioniPrimary (citable) accession number: Q9YH06
Secondary accession number(s): H9BNX0, Q9PUK9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: May 1, 1999
Last modified: September 7, 2016
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.